You need to use pair of sneakers. This sounds more natural. One sneaker is one shoe. One pair of sneakers is 2 - hopefully for left and right foot. So if you say 3 sneakers that's only 3 total (and one missing :( ) AND if you say 3 pairs, then you have 6 shoes in total for 3 outfit changes :)

Interestingly in American English it is also possible to say ‘three pair of sneakers’. ‘Pairs’ is usually still preferred except in some cases such as poker hands, where hands are labeled ‘one pair’ and ‘two pair’. But the singular ‘pair’ doesn’t sound too wrong to us.

In your question, you need to say "to" instead of "which" and drop the comma: "When someone says 'I have three sneakers' to mean "3 pairs of sneakers", does it sound natural to native speakers?"

3 sneakers = 3 shoes. 3 Pairs of sneakers = 3 x 2 Shoes

In English, you would always say "I have 3 pairs of sneakers." as "3 sneakers" means just 3 single sneakers. Shoes are always in pairs. :-) Hope that helps.